title: Saccharomyces cerevisiae 30K microarray

status: Public on Jul 31 2013

city: Seoul

first: miwha

last: Chang

address: anam dong 5ga

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea university

organism: Saccharomyces cerevisiae

technology: in situ oligonucleotide

description: The identical probe sets in 3X20K format microarray are represented in GPL16942.

distribution: custom-commercial

manufacture_protocol: MYcroarray, MI USA


title: Transcription factor qRT-PCR

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

organism: Arabidopsis thaliana

technology: RT-PCR

description: real-time PCR assay using SYBR Green chemistry

distribution: virtual

manufacturer: primers for qRT-PCR were obtained from Eurofins MWG Operon


title: 454 GS FLX Titanium (Eutrema salsugineum)

status: Public on Jul 30 2013

last: GEO

country: USA

organism: Eutrema salsugineum

technology: high-throughput sequencing


title: Agilent-033874 Custom Neotoma lepida eArray (ProbeName version)

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

organism: Neotoma lepida

manufacture_protocol: see manufacturer's web site at http://www.agilent.com/


title: IRCGP Canine 720K v1.0

city: seoul

first: SeungHyun

last: Jung

state: seoul

address: catholic university, medical college, banpo-dong

department: Department of Biochemistry

institute: Catholic University of Korea

organism: Canis lupus familiaris

description:
1. We used a NimbleGen custom 720K canine whole-genome array platform (Roche NimbleGen, Penzberg, Germany), designed from the UCSC dog genome build of May 2005 (Broad/canFam2).
2. This array is comprised of 385,000 probes evenly distributed throughout the unique sequence of the genome as a backbone and an additional ~330,000 probes which were designed based on previously reported dog CNV regions.
3. The average probe spacing for our custom array platform was ~3.3 Kb.
4. The array-CGH experiments were performed according to the manufacturer’s instructions.

manufacture_protocol: see manufacturer's web site www.nimblegen.com


title: 031058-Agilent ATH NAT array

status: Public on Dec 23 2013

city: New York

first: Huan

last: Wang

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

manufacturer: Laboratory of Plant Molecular Biology, Rockefeller University; Agilent Technologies


title: 454 GS FLX (Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819)

status: Public on Jul 29 2013


title: Agilent-023728 Yokoyama-MCMV-103k-v1.0

city: Saint Louis

first: travis

last: Chapa

state: MO

address: 4440 Parkview Place

department: Microbiology

institute: Washington University in St. Louis

organism: Murid betaherpesvirus 1

manufacture_protocol: 103,347 60mer single-stranded probe oligonucleotides were spotted according to Agilent standard method.


title: Agilent-046637 Sus scrofa CGH array

city: Beijing

first: Huimin

last: Kang

state: Beijing

address: Beijing

country: China

institute: China Agriculture University

organism: Sus scrofa

description:
Arrays of this design have barcodes that begin with 16046637 or 2546637.

The ID column represents the Agilent Probe Name.

genome build: Sscrofa10.2


title: Agilent Genotypic Candida albicans 15.7K

city: Würzburg

first: Rebecca

last: Schillig

address: Josef-Schneider-Straße 2 /Bau D15

institute: Institute for Molecular Infection Biology

organism: Candida albicans

manufacture_protocol: See Agilent's website.


title: Agilent Pseudomonas aeruginosa PAO1 Custom Microarray (Probe Name version)

city: Nanjing

first: lixing

last: weng

state: Jiangsu

address: 9 wenyuan road, xianlin

department: School of Geography and Biological Information

institute: Nanjing University of Posts and Telecommunications

organism: Pseudomonas aeruginosa PAO1

manufacture_protocol: see manufacturer's web site


title: AB SOLiD 4 System (Schistosoma mansoni)

organism: Schistosoma mansoni


title: Agilent-017743 Physcomitrella patens agilent microarrays

city: Sheffield

first: Martin-Timothy

last: O'Donoghue

address: Western Bank

department: Department of Animal and Plant Sciences

country: United Kingdom

institute: University of Sheffield

organism: Physcomitrium patens

first: Ralph

last: Quatrano

manufacture_protocol: Microarrays were manufactured according to Agilent protocols. The Physcomitrella array was designed to maximize genome coverage.  The transcripts from the JGI assembly version 1.1 were used (see http://genome.jgi-psf.org/physcomitrella/physcomitrella.download.ftp.html) as input.  There are 35,939 filtered transcripts (combination of predicted models and based on EST evidence) identified from the genome assembly.  The annotations can be downloaded from the JGI web site.  Of the ~36K transcripts probes were designed for 31K; the remaining 4K are either redundant (>99% identical) or composed of low-complexity (simple repeats, poly Q, etc.; probably not real transcripts as they do not produce a meaningful translation) sequences so no high quality probes can be designed.  The array format of the Physcomitrella patens array is a 4 x 44K, and the actual number of user defined probes is 41,384 (the other probes are used for QC). Therefore, the manufacturer repeated a subset of 31K (picked at random) to fill out the 41, 384 probe real estate. This microarray was commissioned by the Ralph Quatrano group (Washingtom University) and they gave us permission to use this microarray in our study.


title: Illumina MiSeq (Schistosoma mansoni)


title: Agilent-023673 Custom Oryzias latipes (Japanese medaka) 4x44K microarray

city: xiamen city

first: geng

last: hong

address: School of Life Sciences, Xiamen University,

department: Biology

institute: School of life sciences

organism: Oryzias latipes

manufacture_protocol: Aglient Custom Gene Expression Microarray, 4x44K. Catalog # G2514F. Manufacturer's web site at http://www.agilent.com/


title: RMIT University Salvia Subtracted Diversity Array (SDA)

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

country: Australia

institute: RMIT University

organism: Salvia

technology: spotted DNA/cDNA

description:
Specific for all species belonging to the Salvia genus.

Only 10 subtracted fragments (clones) were sequenced.

distribution: non-commercial

manufacturer: Alexandra Olarte/Edwin Pang/Nitin Mantri, RMIT University

manufacture_protocol:
Plant material and genomic DNA extraction: In order to obtain a genomic DNA (gDNA) representation for the subtraction, a total of 151 species including angiosperms and non-angiosperms were sourced. Non-angiosperms were collected from Toolangi State Park, Victoria (Australia) and identified (Duncan and Isaac, 1994). Angiosperms were obtained only from verified nursery species; a total of 126 species were sourced to represent all angiosperm clades. In addition, a total of ten Salvia species (42 plants) were sourced to represent the different centres of diversity around the world. Salvia miltiorrhiza and S. sinica Migo plants were obtained from seeds which were used in a previous study (Li et al., 2009). The other Salvia species were obtained from verified specimens from various plant nurseries. Total DNA was extracted from fresh leaves using a modification of the standard CTAB procedure (Doyle and Doyle, 1987) and subsequent cleanup was performed by using the DNeasy® column of the DNeasy® Plant Mini Kit (Qiagen) following the protocol in the user manual.The quantity of DNA was measured using Eppendorf spectrophotometer whilst the quality/integrity was assessed by 1.5% agarose gel electrophoresis.

Genomic DNA subtraction and library construction: All DNA samples were pooled based on the Angiosperm Phylogeny Group (2009) classification (Bremer et al., 2009) in order to obtain representations of the following seven groups: Salvia (Tester pool), non-angiosperms, Monocots, Magnoliids, Rosids, Asterids (excluding Lamiaceae), and Eudicots not placed in either Rosids or Asterids subclades (Eudicots and Core Eudicots). Subtraction was performed using the PCR-Select™ cDNA Subtraction Kit (Clontech). The Salvia pool (tester) was represented by equal amounts of DNA extracted from 42 different plants of which 25 were Salvia miltiorrhiza (5 plants from 5 different lines). The driver pool was obtained by bulking 700 ng of each representation with the exception of the Salvia pool. Subsequently, 4 μg of pooled gDNA from each group was restriction digested in a 50 μL reaction using 5U of HaeIII and AluI (New England Biolabs). As previously described (Mantri et al., 2012), the digested diver gDNA pool was subtracted from digested tester gDNA pool to isolate Salvia-specific DNA. The Salvia-specific DNA fragments were cloned into pGEM-T® Easy Vector (Promega, Madison, WI) and transformed into Escherichia coli JM109 competent cells (Promega, Madison, WI).

Microarray construction and printing: The cloned inserts were PCR amplified from the corresponding plasmid using nested primers 1 and 2R (Clontech). After that, PCR products were precipitated in 96% ethanol and 3 M sodium acetate (pH 5.2). The precipitation was carried out at -20 °C overnight. The pellets obtained were washed with 70% ethanol, air dried and resuspended in 10 µl of 50% DMSO. Finally, a total of 285 clones with inserts ranging from 250 bp to 1000 bp, were transferred individually into a 384-well plate (Genetix, Hampshire, UK) together with positive and negative controls. Among the positive controls were three housekeeping genes (ribulose-1,5-bisphosphate carboxylase/oxygenase, ribosomal RNA, and chlorophyll a/b binding protein) sourced from Cicer arietinum (Coram and Pang, 2005). The 285 clones together with the controls were printed on aminosilane-coated slides using a BioRobotics® MicroGrid II Compact arrayer (Genomic Solutions) at RMIT University, Australia. Eight subarrays were gridded on a Corning® GAPS II coated slide (Corning Incorporated Life Sciences, Acton, MA). Each subarray was composed of 285 samples and 15 controls.


title: Agilent-032261 FZ_IBG-1_Avinosum_Ver1

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

organism:
Bacillus subtilis subsp. subtilis str. 168
Rhodobacter capsulatus SB 1003
Escherichia coli str. K-12 substr. MG1655
Allochromatium vinosum DSM 180

description: Allochromatium vinosum DSM 180T (NC_013851), Escherichia coli MG1655 (NC_000913), Bacillus subtilis str. 168 (NC_000964), Rhodobacter capsulatus SB 1003 (NC_014034)

manufacture_protocol: see Agilent Technologies


title: NimbleGen_Cryptomeria japonica_23k both strand array

city: Tsukuba

first: Norihiro

last: Futamura

state: Ibaraki

address: 1 Matsunosato

country: Japan

institute: Forestry and Forest Products Research Institute (FFPRI)

organism: Cryptomeria japonica

description:
2007-10-10_GFC149_SUGI_expr. Probe sets for genes of Cryptomeria japonica were designed from assembled ESTs, consisting of 10,655 tentative contigs and 12,227 singletons. Each probe set consisted of eight 60-mer probe pairs (PM only) per gene. Probe sets were designed for both strands of assembled ESTs.
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files.

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: Illumina HiSeq 2000 (Ornithorhynchus anatinus)

status: Public on Jul 26 2013

organism: Ornithorhynchus anatinus


title: Agilent-020128 Ca21_GE_2.0 [Orf version]

status: Public on Jul 28 2013

city: San Francisco

first: Changbin

last: Chen

state: California

address: HSE450, 513 Parnassus Avenue

department: Department of Microbiology & Immunology

institute: University of California, San Francisco

description:
This is an expression array designed against the assembly 21 Orf list, including the alpha locus.  Most orfs have 2 probes each, while 860 orfs which had discordant values between original probes have been assigned 5 probes/orf to identify non-discordant probes.  "

Arrays of this design have barcodes that begin with 16020128 or 2520128.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software."

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface)."

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions."


title: SABiosciences total CD4SP thymoctye PCR assay panel

status: Public on Jul 27 2013

city: Bethesda

first: Jung-Hyun

last: Park

state: MD

address: 10 Center Dr

department: EIB

institute: NIH/NCI

organism: Mus musculus

description:
WT-Ik7Tg total CD4SP thymocyte PCR assay panel
SABiosciences RT² Profiler panel of PCR assays.

manufacture_protocol: see manufacturer's website


title: FZ_IBG-1_Goxydans_10K_Ver1

organism: Gluconobacter oxydans 621H

technology: spotted oligonucleotide

description: G.oxydans 621H, based on the genome sequence entry NC_006677

manufacturer: Operon (Cologne, Germany) and Microarrays Inc. (Huntsville, USA)

manufacture_protocol: spotted with 70-mer oligonucleotides obtained from Operon (Cologne, Germany)


title: SABiosciences immature and mature CD4SP thymoctye PCR assay panel

description:
WT-Ik7Tg immature CD4SP thymocyte PCR assay panel
SABiosciences RT² Profiler panel of PCR assays.


title: Agilent-042984 Pathogen Version 3

status: Public on Jul 25 2013

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

organism: Viruses

description:
Pathogen microarray version 3  035096

Arrays of this design have barcodes that begin with 16042984 or 2542984.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent-024722 Bovine miRNA Microarray Rel.13.0

status: Public on Jul 24 2013

city: Nagareyama

first: Wataru

last: Kurihara

state: Chiba

address: Higashifukai 105

institute: Biomatrix Research Inc.

organism: Bos taurus

description:
Arrays of this design have barcodes that begin with 16024722 or 2524722.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent-036466 Bovine miRNA Microarray Rel.17.0 8x60K

description:
Arrays of this design have barcodes that begin with 16036466 or 2536466.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent Homo sapiens 37K DiscoverPrint_19742

status: Public on Jul 23 2013

city: Amsterdam

first: Paul

last: Roepman

address: Science Park 406

country: Netherlands

institute: Agendia

organism: Homo sapiens

manufacture_protocol: Microarrays were prepared by Agilent technologies using their Agilent SurePrint Technology. Briefly, 60-mer oligonucleotides are synthesized base-by-base in repetitive print layers on a solid glass substrate, using standard phosphoramidite chemistry.


title: Eurogentec Neisseria meningitidis MC58 SP-Nmeningitidis-PCR-V1

city: Marcy l'Etoile

first: Bachra

last: Rokbi

address: 1541 Av M Mérieux

country: France

institute: sanofi pasteur

organism: Neisseria meningitidis MC58

manufacture_protocol: See manufacturer's web site.


title: Agilent-023681 yanqumei - Aspergillus fumigatus custom 8×15K

status: Public on Jul 22 2013

city: beijing

first: jianghong

last: yan

state: beijing

address: NO.1 West Beichen Road

institute: Institute of Microbiology

organism: Aspergillus fumigatus

description:
Arrays of this design have barcodes that begin with 16023681 or 2523681.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Illumina Genome Analyzer II (Larix kaempferi)

status: Public on Jul 19 2013

last: GEO

organism: Larix kaempferi


title: Agilent-035546 FZ_IBG-1_Avinosum_Ver2

organism:
Corynebacterium glutamicum
Pseudomonas putida KT2440
Pseudomonas aeruginosa PAO1
Bacillus subtilis subsp. subtilis str. 168
Allochromatium vinosum DSM 180

description: Allochromatium vinosum DSM 180T (NC_013851), Corynebacterium glutamicum (NC_006958), Bacillus subtilis str. 168 (NC_000964), Pseudomonas putida KT2440 (NC_002947), Pseudomonas aeruginosa PAO1 (NC_002516)


title: NimbleGen-hCMV-4X72K tiling array [090115_CMV_ES_ChIP]

status: Public on Jul 17 2013

first: Desiree

last: Tillo

address: 41 Center Dr, Room D310

organism: Human betaherpesvirus 5

description:
Probes on the array are based on the hCMV TB40E sequence (NCBI GenBank: EF999921)
Both strands of the hCMV TB40E genome sequence (NCBI GenBank: EF999921) are tiled identically across each subarray at ~7 bp resolution and >99% coverage using 32,562 overlapping isothermal 50–60mer oligonucleotide probes (OID19196). The remaining space (6,876 probes) is filled with random and standard quality control probes.


title: Agilent-021422 S_cerevisiae_incl_control

status: Public on Jul 18 2013

city: Clayton

first: traude

middle: Helene

last: Beilharz

address: Monash University

department: Biochemistry & Molecular Biology

institute: Monash University

organism: Saccharomyces cerevisiae

description:
Arrays of this design have barcodes that begin with 16021422 or 2521422.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent-027999 Custom Fundulus heteroclitus array

city: Gainesville

first: Christopher

middle: Joseph

last: Martyniuk

state: FL

address: CEHT Mowry Road

department: Physiological Sciences

institute: UF

organism: Fundulus heteroclitus


title: Applied Biosystems Human TaqMan Low Density Array (TLDA)

city: Boston

first: Aldo

last: Roccaro

state: MA

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

description: Applied Biosystems 7900HT instrument


title: Illumina Genome Analyzer IIx (Drosophila simulans)

organism: Drosophila simulans


title: Illumina HiSeq 2000 (Bacteroides cellulosilyticus)

organism: Bacteroides cellulosilyticus


title: Illumina HiSeq 2000 (Synechococcus sp. PCC 7002)

organism: Picosynechococcus sp. PCC 7002


title: Hyalella azteca 135k array version 1

first: Helen

middle: C

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

organism: Hyalella azteca

description: This microarray was designed following 454 sequencing and de-novo assembly of the Hyalella azteca transcriptome.  The version of the assembly that was used to create the array was an early assembly which was later updated with addition sequences before it was uploaded to GenBank.  Therefore, the probes do not directly correspond with sequences in GenBank.

manufacture_protocol: see NimbleGen website


title: Illumina HiSeq 2000 (Pseudomonas fluorescens SBW25)

status: Public on Jul 16 2013

organism: Pseudomonas [fluorescens] SBW25


title: Exiqon Human miRCURY LNA Array (v.16.0)

city: Los Angeles

first: Steven

middle: M

last: Dubinett

state: CA

address: 10833 Le Conte Avenue

department: Medicine-Pulmonary

institute: University of California, Los Angeles

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: Exiqon array (Item # 20-1122; Lot#34001.03, 6th generation (product#208401-A Lot#6000)


title: Illumina HiSeq 2000 (Talaromyces marneffei PM1)

organism: Talaromyces marneffei PM1


title: Affymetrix custom Bradyrhizobium japonicum strain USDA 110 19K array

status: Public on Mar 15 2006

city: Zürich

first: Hans-Martin

last: Fischer

address: Vladimir-Prelog-Weg 4

country: Switzerland

institute: ETH Zürich

organism: Bradyrhizobium diazoefficiens USDA 110

description: 11 um high-density, whole genome array representing all 8317 annotated B. japonicum strain USDA 110 open reading frames plus 51 RNA genes and intergenic regions of >40 bp

first: Hauke

last: Hennecke

first: Felix

last: Hauser


title: Illumina Genome Analyzer (Panonychus citri)

organism: Panonychus citri


title: Illumina HiSeq 2000 (Saccharopolyspora erythraea)

status: Public on Jul 15 2013

organism: Saccharopolyspora erythraea


title: NimbleGen Plasmodium falciparum 3x720K array v1.0

city: Sao Paulo

first: Wania

middle: Rezende

last: Lima

state: Sao Paulo

address: Rua Matão, travessa 14, n 321

department: Physiology

country: Brazil

institute: University of São Paulo

organism: Plasmodium falciparum

description:
PlasmoDB genome build, version 7.0
Pfalciparum_PfNFYB_Brazil.ndf
Pfalciparum_PfNFYB_Brazil.pos


title: SABiosciences Human breast cancer pathway-focused miScript miRNA PCR array

city: Houston

first: Laura

last: Camacho

address: One Baylor Plaza

institute: Baylor College of Medicine

organism: Homo sapiens

description:
PCR assay
miScript miRNA PCR Array


title: Agilent-027586 Aspergillus oryzae RIB40 array

city: Gothenburg

first: D.B.R.K. Gupta

last: Udatha

state: Sweden

address: Medicinaregatan 9C

department: Department of Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

organism: Aspergillus oryzae RIB40


title: Agilent-033881 P. indica and A. thaliana 63K Pindica_Athal_MPI_UL

status: Public on Jul 21 2013

city: Regensburg

first: Urs

last: Lahrmann

address: Am Biopark 9

department: Project Group Personalized Tumor Therapy

institute: Fraunhofer ITEM

organism:
Arabidopsis thaliana
Serendipita indica

description:
Piriformospora indica gene expression chip with optimized probes plus Arabidopsis genes

Arrays of this design have barcodes that begin with 16033881 or 2533881.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Saccharomyces 20080514MD_PMC

status: Public on Jul 12 2013

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

organism:
Saccharomyces bayanus
Saccharomyces cerevisiae

description: SBSC print, a multi-organism print.

manufacturer: Lewis-Sigler Institute Microarray Facility

manufacture_protocol:
The following parameters were used to manufacture the printed array named "20080514MD_PMC"
Printer: Arrayer 250A
Array Configuration: (columns X rows) 48 sectors ( 4 X 12 spotted) Standard 48 tip
Spot Columns per Sector: 16
Spot Rows per Sector: 17
Column Spacing: 235
Row Spacing: 240
Plate Orientation: rotated 90 degrees clockwise (P1 top-left, A1 top-right)
Printhead Dip Dynamics: top to bottom, right to left
Sector Spotting Dynamics: left to right, top to bottom
Number of Slides: 254
Plates used in this print, in order.
PLATEID PLATENAME PLATE_VISITS IS_FLIPPED
100700 SBSC_SONIC_1  1
100516 HYBRIDSC_4  1
100527 HYBRIDSC_15  1
100517 HYBRIDSC_5  1
100510 HYBRIDSB_11  1
100524 HYBRIDSC_12  1
100509 HYBRIDSB_10  1
100528 HYBRIDSC_16  1
100512 HYBRIDSB_13  1
100525 HYBRIDSC_13  1
100506 HYBRIDSB_7  1
100529 HYBRIDSC_17  1
100520 HYBRIDSC_8  1
100518 HYBRIDSC_6  1
100704 SBSC_SUPP_1  1
100522 HYBRIDSC_10  1
100519 HYBRIDSC_7  1
100504 HYBRIDSB_5  1
100511 HYBRIDSB_12  1
100521 HYBRIDSC_9  1
100526 HYBRIDSC_14  1
100513 HYBRIDSC_1  1
100508 HYBRIDSB_9  1
100507 HYBRIDSB_8  1
100505 HYBRIDSB_6  1
100523 HYBRIDSC_11  1
100515 HYBRIDSC_3  1
100501 HYBRIDSB_2  1
100500 HYBRIDSB_1  1
100503 HYBRIDSB_4  1
100502 HYBRIDSB_3  1
100514 HYBRIDSC_2  1
100700 SBSC_SONIC_1  1


title: Nimblegen Coccidioides immitis RS 12x135K array

status: Public on Jul 11 2013

city: London

first: Akul

last: Singhania

address: 1 Midland Road

institute: The Francis Crick Institute

organism: Coccidioides immitis RS

description:
Standard protocol for NimbleGen 12x135K array
100722 CIRS TK EXP.ndf
100722 CIRS TK EXP.ngd


title: [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array [Custom CDF: ATH1121501_At_TAIRG, Version 14.0.0]

city: Sutton Bonington

first: Simon

middle: Peter

last: Pearce

state: Leicestershire

address: Sutton Bonington Campus

department: Plant and Crop Sciences

institute: University of Nottingham

organism: Arabidopsis thaliana

description: v14.0.0 Arabidopsis CustomCDF from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF

relation: Affiliated with: GPL198 (Alternative CDF [official])


title: Illumina Genome Analyzer II (Bacteroides caccae ATCC 43185; Bacteroides ovatus ATCC 8483; Bacteroides thetaiotaomicron VPI-5482; Clostridium symbiosum; Collinsella aerofaciens ATCC 25986; Desulfovibrio piger GOR1; Escherichia coli str. K-12 substr. MG1655; Eubacterium rectale ATCC 33656; Marvinbryantia formatexigens DSM 14469)

last: GEO

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656
Desulfovibrio piger GOR1


title: Illumina MiSeq (Bacteroides caccae ATCC 43185; Bacteroides ovatus ATCC 8483; Bacteroides thetaiotaomicron VPI-5482; Clostridium symbiosum; Collinsella aerofaciens ATCC 25986; Desulfovibrio piger GOR1; Escherichia coli str. K-12 substr. MG1655; Eubacterium rectale ATCC 33656; Marvinbryantia formatexigens DSM 14469)


title: Illumina MiSeq (Bacteroides caccae ATCC 43185; Bacteroides ovatus ATCC 8483; Bacteroides thetaiotaomicron VPI-5482; Clostridium symbiosum; Collinsella aerofaciens ATCC 25986; Escherichia coli str. K-12 substr. MG1655; Eubacterium rectale ATCC 33656; Marvinbryantia formatexigens DSM 14469)

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656


title: Illumina HiSeq 2000 (Bacteroides caccae ATCC 43185; Bacteroides ovatus ATCC 8483; Bacteroides thetaiotaomicron VPI-5482; Clostridium symbiosum; Collinsella aerofaciens ATCC 25986; Escherichia coli str. K-12 substr. MG1655; Eubacterium rectale ATCC 33656; Marvinbryantia formatexigens DSM 14469)


title: Illumina HiSeq 2000 (Bacteroides caccae ATCC 43185; Bacteroides ovatus ATCC 8483; Bacteroides thetaiotaomicron VPI-5482; Clostridium symbiosum; Collinsella aerofaciens ATCC 25986; Desulfovibrio piger GOR1; Escherichia coli str. K-12 substr. MG1655; Eubacterium rectale ATCC 33656; Marvinbryantia formatexigens DSM 14469)


title: Agilent-045857 Melita_final_2012 [Probe name version]

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

institute: CSIRO

organism: Melita plumulosa

description:
QAed version of probe created from amphipod assembly project

Arrays of this design have barcodes that begin with 16045857 or 2545857.


title: Illumina HiSeq 2000 (Boea hygrometrica)

status: Public on Jul 10 2013

organism: Dorcoceras hygrometricum


title: Agilent-033850 Tetranychus urticae 63K array

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

organism: Tetranychus urticae

manufacture_protocol: See the manufacturer's web site at http://www.agilent.com/.


title: Nimblegen Salmonella Typhimurium LT2 TI99287 60mer

status: Public on Jul 09 2013

first: Geoffrey

last: Gonzalez

address: 55 Fruit St

department: Infectious Diseases

institute: Massachusetts General Hospital

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

description: Catalog design for Salmonella typhimurium LT2 (Taxonomy Id: 99287) covering NC_003197, NC_003277. Probes selected for 4527/4527 sequences. Median number of probes/sequence is 17 with an average of 17.00. Each probe will be replicated 5 times on the chip. Probes are randomly distributed over the surface of the array. Unused features have been filled with randomly generated probes of comparable GC content.


title: Human MicroRNA Card Set v2.0 array

city: Bethesda

first: GEO

last: admin

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description: TaqMan PCR assay comprising Cards A and B.

manufacture_protocol: See manufacturer's website (http://www.appliedbiosystems.com/).


title: MRA-1002_miRMouse_16

first: Christoph

last: Eicken

state: TX

address: 2575 W. Bellfort

institute: LC Sciences, LLC

organism: Mus musculus

distribution: commercial

manufacture_protocol: Mouse miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 16.0. Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes are made by in situ synthesis using PGR (photogenerated reagent) chemistry.


title: Illumina HiSeq 2000 (mouse gut metagenome)

organism: mouse gut metagenome


title: Illumina HiSeq 2000 (Musa acuminata)

status: Public on Jul 05 2013

organism: Musa acuminata


title: 080829_B_taurus_JK_EXP

status: Public on Jul 04 2013

city: Glasgow

first: William

last: Weir

address: Room 220, Henry Wellcome Building, Garscube Campus, Bearsden Road

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

organism:
Theileria annulata
Bos taurus

description:
385K expression array representing all available RefSeq RNA sequences plus additional EST sequences for Bos taurus and including all predicted coding sequences of the bovine intracellular parasite Theileria annulata. 60 mer probe array, five probes per gene, replicated in 2 blocks.
native array description file: 080829_B_taurus_JK_EXP.ndf
native array description file: 080829_B_taurus_JK_EXP.ngd

manufacture_protocol: Expression array - 1plex 385k expression array


title: [AraGene-1_0-st] Arabidopsis Gene 1.1 ST Array [CDF: aragene10st_At_TAIRG version 16]

status: Public on Jul 08 2013

manufacture_protocol: This is identical to GPL17416 but a custom cdf environment was used to extract data. The custom CDF file is based on Ensembl genes (from http://brainarray.mbni.med.umich.edu version 16). The custom cdf is linked below as a supplementary file.


title: Illumina Genome Analyzer IIx (Bos indicus)

status: Public on Jul 02 2013

organism: Bos indicus


title: Agilent-019587 Eca4444Array2

status: Public on Jul 03 2013

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

organism: Pectobacterium atrosepticum

manufacture_protocol: Agilent inkjet technology, 60mer oligos


title: [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array (mm4302daiplusv5cdf)

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

description: Dai et al., NAR (2005), 33(20):e175 and de Leeuw et al.,BMC Res Notes. 2008; 1: 66


title: Illumina HiSeq 2000 (Procotyla fluviatilis)

organism: Procotyla fluviatilis


title: NimbleGen Campylobacter jejuni NCTC11168 Whole-Genome microarray [080328_C_jejuni_NCTC_11168_expr]

city: Madison

first: Inc

last: Nimblegen Systems

state: WI

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

description:
The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features.  The .ndf and .ngd files are submitted as supplementary files.
Genome Accession number: NC_002163


title: Affymetrix QunatiGene Plex Assay 2.0 [Pannels 321347 & 321389]

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

description: custom-made Multiplex assay


title: NimbleGen Human DNA Methylation 2.1M Deluxe Promoter Array [100929_HG19_Deluxe_Prom_Meth_HX1]

city: Dallas

first: Qiuyue

last: Chen

address: 5323 Harry Hines Blvd.

department: Molecular Genetics

institute: UT Southwestern Medical Center

organism: Homo sapiens

description:
Annotation in this record is based on NCBI human build 19.
designname=100929_HG19_Deluxe_Prom_Meth_HX1
designid=537151

manufacture_protocol: see manufacturer's website (http://www.nimblegen.com/products/methylation/tutorial/index.html)


title: Estrogen Receptor Signaling PCR Array PAHS-005

city: coventry

first: dimtiris

last: grammatopoulos

address: gibbet hill road

institute: warwick medical school

description: PCR assay


title: Agilent-035096 Pathogen_version2

status: Public on Jul 01 2013

city: Beijing

first: wang

last: liang

address: 7A North Yongchang Road BDA

institute: BioChainBJ

organism: Viruses

description:
Pathogen_version2

Arrays of this design have barcodes that begin with 16035096 or 2535096.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

manufacture_protocol: see manufacturer's web site at http://www.agilent.com/


title: Illumina HiScanSQ (Glycine max)

organism: Glycine max


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray ENSG Version 17.1]

relation: Alternative to: GPL570 (Alternative CDF [official])

manufacture_protocol: see manufacturer's protocol


title: febit Homo Sapiens miRBase 14.0

city: Tarragona

first: Anna

last: Arola-Arnal

state: Tarragona

address: Campus Sescelades. C/Marcel.lí Domingo s/n

country: Spain

institute: Universitat Rovira i Virgili

manufacture_protocol: MicroRNAs (miRNAs) are endogenous, non-coding RNAs that play a fundamental role in gene regulation and have critical functions across various biological processes. Pairing to mRNAs of protein-coding genes, they direct posttranscriptional repression by altering the stability or translational efficiency of their target mRNAs.  Recent studies indicate that miRNAs are involved in the development of human malignancies, suggesting that they represent a promising new class of cancer biomarkers. Identifying miRNAs involved in specific cancers could provide useful diagnostic information, allow disease classification and reveal potential treatment targets.  MPEA: On-Chip Labeling for Highest Sensitivity  Enzymatic labeling assay requires minimal sample amount  In addition to the standard hybridization of pre-labeled RNA, the microfluidic Geniom Biochip enables a highly sensitive enzymatic labeling protocol.  MPEA benefits  * Higher sensitivity and specificity  * miRNA hybridization without preceding treatment like enrichment, PCR -based amplification or labeling eliminates potential bias  * High discriminatory power  * Minimal amount of sample RNA needed (more than or equal 20 ng total RNA)  * Easy to use protocol for Geniom RT Analyzer    The unique Microfluidic Primer Extension Assay (MPEA) uses unlabeled miRNAs for hybridization. In a second step, Klenow fragment of DNA polymerase I is added directly into the channels of the microfluidic chip, where the specific elongation of the bound miRNAs takes place.  The method combines the specificity of a hybridization assay with the discriminatory power of an enzymatic extension and reduces the required sample amount to a minimum.  Details provided at www.febit.com


title: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)


title: Illumina HiSeq 2000 (Populus trichocarpa)

organism: Populus trichocarpa


title: Agilent-025219 HELP mm8 array [condensed version]

city: Tsukuba

first: Rieko

last: Ikeda

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Center

institute: RIKEN

description:
Arrays of this design have barcodes that begin with 16025219 or 2525219.
Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.
The ID column represents the unique MM8MSPIS ACCESSION_STRING. The full array layout file is linked as a supplementary file.


title: Agilent-013205 44Kx1 Expression Array [Probe Name version]


title: [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array [CDF: Brainarray ENSG Version 13.0]


title: NimbleGen Mus musculus array [2006-09-11_KB_HELP1]

description:
Design Name: 080718_Pfluor_Bbc6_expr
Design ID: 7919
Native array description file: 2006-09-11_KB_HELP1.ndf
Native array description file: 2006-09-11_KB_HELP1.ngd
Native array description file: 2006-09-11_KB_HELP1.pos

manufacture_protocol: Propriety in situ oligonucleotide synthesis.


title: Filgen S. pombe 5K Array

city: Tokyo

first: Akira

last: Yamashita

address: Hong

department: Department of Biophysics and Biochemistry

institute: University of Tokyo

organism: Schizosaccharomyces pombe

manufacture_protocol: See manufacturer's website at http://www.filgen.jp.


title: Agilent-019033 Human Epilepsy Candidate Gene Array v1 array (Probe Name version)

city: Houston

first: Tara

middle: Leah

last: Klassen

address: One Baylor Plaza

department: Neurology

institute: Baylor College of Medicine

description:
Agilent-019033 ICE
exon+-1kb plus gene and genome
Array layout was auto-generated in e-Array(Agilent) Microarray design software targeting candidate genes for epilepsy using a high-density exonic coverage plus genomic backbone.
Arrays of this design have barcodes that begin with 16019033 or 2519033.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction probe name.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Agilent-019456 MCD2008 Expression Array [Probe Name version]

description:
The full array layout file is linked as a supplementary file.
Arrays of this design have barcodes that begin with 16019456 or 2519456.


title: NuGO array (mouse) NuGO_Mm1a520177

city: Freising

first: Jana

last: Hemmerling

state: Bavaria

department: ZIEL

institute: Technische Universität München

description: CDF file was created by Microarray Lab at the Molecular and Behavioral Neuroscience Institute at the University of Michigan.

manufacture_protocol: This array has been designed by NuGO and manufactured by Affymetrix.


title: Agilent-019033 Human Epilepsy Candidate Gene Array v1 array (Feature Number version)

description:
Agilent-019033 ICE
exon+-1kb plus gene and genome
Array layout was auto-generated in e-Array(Agilent) Microarray design software targeting candidate genes for epilepsy using a high-density exonic coverage plus genomic backbone.
Arrays of this design have barcodes that begin with 16019033 or 2519033.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.


title: Saccharomyces cerevisiae 3x20K Microarrays

status: Public on Apr 03 2013

city: Seoul

first: miwha

last: Chang

address: anam dong 5ga

department: School of Life Sciences and Biotechnology

institute: Korea university

organism: Saccharomyces cerevisiae

description: The identical probe sets in 30K format microarray are represented in GPL17508.

manufacture_protocol: MYcroarray , MI. USA.


title: NimbleGen Human ChIP-chip 3x720K RefSeq Promoter Arrays [100718_HG18_Refseq_Prom_ChIP]

city: ROCHESTER

first: Haojie

last: Huang

state: MINNESOTA

address: 200 1st ST SW

institute: Mayo Clinic

description:
Format: 3x720K. Source: UCSC. Build: HG18. Probe length: 50-75mer. Median probe spacing: 100bp
Catalog number: 05924405001


title: NimbleGen Fusarium fujikuroi annotation version 1 gene expression array [110407_UG_Ffujikuroi_expr]

first: Ulrich

last: Guldener

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

organism: Fusarium fujikuroi

description:
NimbleGen design name: 110407_UG_Ffujikuroi_expr_HX12
Native array description file: 110407_UG_Ffujikuroi_expr.ndf
Native array description file: 110407_UG_Ffujikuroi_expr.ngd

manufacture_protocol: High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.


title: miRXplore TM Microarray (836)

status: Public on Nov 28 2012

city: Bergisch Gladbach

first: Silvia

last: Rueberg

address: Friedrich-Ebert-Str. 68

department: Genomic Services

institute: Miltenyi Biotec GmbH

organism:
Homo sapiens
Mus musculus
Rattus norvegicus

description: The miRXplore TM Microarray is composed of 5668 DNA oligonucleotides with a sequence being reverse complement to the respective mature miRNA or control RNA, representing a total of 1320 miRNA sequences and 95 controls with all probes spotted in quadruplicates. The 1320 miRNA sequences covered sequence-verified miRNAs of the species human (735), mouse (587) and rat (429), as well as viral miRNAs (150) as deposited in the miRBase sequence database version 10.0. The 97 positive and negative control probes were chosen as follows. Three sets of controls, miRControl 1 (four sequences used to assess efficiency and sensitivity of labelling), miRControl 2 (single sequence used to assess efficiency of small RNA enrichment) and miRControl 3 (43 sequences used to normalize signal intensities across different samples and arrays) were artificial sequences chosen not to be present in any of the human, mouse, rat or viral genomes. A fourth set of positive controls presented 36 positive small but non-miRNA sequences including probes e.g., for 5.1 sRNA, tRNAs, and U6 RNAs. A fifth set of oligonucleotides included 13 negative controls like different single or double mismatch, antisense, or scrambled miRNA sequences. Microarrays were manufactured by Miltenyi Biotec. Briefly, 1.2 nl of 10 µM HPLC purified, 5’ amino-modified DNA oligonucleotides (Metabion) were spotted on aminopropyltrimethoxysilane- / phenylendiisothiocyanate-coated glass slides in quadruplicates using a customized piezoelectric spotter.

first: Bernhard

last: Gerstmayer

first: Andreas

last: Bosio

manufacture_protocol: Defined 200-400 bp fragments of selected cDNAs were generated by RT-PCR, cloned and sequence-verified. Amplified and purified cDNA inserts were spotted in quadruplicate on PIQOR slides using a proprietary piezoelectric spotter. The PIQOR slides were coated in a 2-step process generating a surface which covalently binds DNA molecules.


title: Illumina Infinium 20K Canine SNP Beadchip

status: Public on Jul 03 2012

city: Bethesda

first: Heidi

middle: G

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

organism: Canis lupus familiaris

technology: oligonucleotide beads

description: Based on Dog Assembly CanFam2.

manufacture_protocol: See manufacturer's website (www.illumina.com).


title: HMS Drosophila ChIP-seq

status: Public on Aug 01 2008

city: Boston

first: Peter

middle: J

last: Park

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

organism: Drosophila melanogaster

technology: other

description: Solexa sequencing


title: Clostridium thermocellum ATCC 27405 HX12 array (12 x 135k array probe ID)

status: Public on Jan 01 2013

city: Oak Ridge

first: Charlotte

last: Wilson

state: Tennessee

address: 1 Bethel Valley Road

department: Biosciences Bldg 1520

country: New Zealand

institute: ORNL

organism: Acetivibrio thermocellus ATCC 27405

description:
Custom array
GPL11186_080724_C_thermo_27405_expr.ndf
GPL11186_080724_C_thermo_27405_expr.ngd

manufacture_protocol: see manufacturer's web site www.nimblegen.com


title: [CB1190a520768F] Affymetrix Pseudonocardia dioxanivorans strain CB1190 Array

status: Public on Feb 21 2012

city: Berkeley

first: Ariel

last: Grostern

address: 209 O'Brien Hall

department: Civil & Environmental Engineering

institute: UC Berkeley

organism: Pseudonocardia dioxanivorans CB1190

manufacture_protocol: Affymetrix's protocol (see web site)


title: Tiling design for chromosome X, 2L and 4 for D. melanogaster (11/30/04)

status: Public on Aug 01 2007

description: ChIP design of chromosomes 4, X, and 2L from Drosophila tiled at 100bp spacing.

first: Mitzi

middle: I

last: Kuroda


title: Tiling design for chromosome X, 3R and 4 for D. melanogaster

status: Public on Sep 01 2007


title: NimbleGen_2005-05-10_Plasmodium_3D7_WG

status: Public on May 18 2009

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

organism: Plasmodium falciparum

description:
Annotation in this record based on NCBI Plasmodium falciparum 3D7 strain 2005-05-10
Initial oligos were selected at 4bp interval in clusters of 10 oligos.  Masking for repetitive elements was done by generating a histogram of 15-mer frequency in the genome and removing oligos with an average 15-mer frequency greater than 100. Oligos were of variable length (45bp to 83bp, median length of 56bp) and the median Tm was 68.7°C. Uniqueness was ascertained by determining the number of exact 45-mer matches of each oligo in the genome. The best oligo from each cluster of 10 was selected based on average 15-mer frequency, uniqueness, Tm, and base pair composition rules. The final set of oligos was arranged using ArrayScribe array design software (NimbleGen Systems Inc.). Arrays were constructed as described previously/


title: NimbleGen 2.1M Maize Methylation Array

status: Public on Nov 21 2011

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

organism: Zea mays

description:
Order ID#: OID29684
Native array description file: 100629_Zea_Mays_NS_CGH_HX1.ndf
Native array description file: 100629_Zea_Mays_NS_CGH_HX1.pos
The sequences of the oligonucleotides are available in the supplementary .ndf file.
B73 RefGen_v2 assembly


title: Tiling design for chromosome X, 2L and 4 for D. melanogaster

status: Public on Aug 03 2007

state: MA

description: ChIP design of chromosomes 4, X, and 2L from Drosophila tiled at 100bp spacing.  All of chr4 and chrX are covered. Only first 19.2 Mb of 2L are covered by this design.


title: FL003 - INDAC Drosophila melanogaster 14.5K long oligo array

status: Public on Mar 04 2009

city: Cambridge

first: Bettina

last: Fischer

address: Tennis Court Road

department: Systems Biology Centre

institute: Unversity of Cambridge

description: Array mapping available at the FlyChip_long_oligonucleotide_003 (FL003) - INDAC page at the Flychip website.

first: Steven

last: Russell

first: Lisa

middle: A

last: Meadows

first: Richard

middle: P

last: Auburn

first: Gos

last: Micklem

first: Roslin

first: Debashis

last: Rana

first: Santiago

middle: S

last: Matila

last: Sykacek

first: David

last: Kreil

manufacture_protocol: FL003 microarrays were printed using the Genetix Qarray2 contact-printing instrument and 48 Genetix aQu75 split-pins on FMB PowerMatrix slides. Probe DNA was dissolved in 150 mM NaPO4. Full details on Flychip website (http://www.flychip.org.uk/).


title: NimbleGen Human 2.0M array [091020_HG19_CHARM_HX1]

status: Public on Aug 29 2011

city: Madison

first: Inc

last: Nimblegen Systems

address: 504 S. Rosa Road

institute: NimbleGen Systems, Inc.

description:
Annotation based on UCSC human genome assembly Feb 2009 (hg19)
designname=091020_HG19_CHARM_HX1
designid=10816


title: [SynComm1a520717] SynComm1: Synthetic Human Gut Community GeneChip, v1.0

status: Public on Dec 18 2009

city: Saint Louis

first: Nathan

last: McNulty

address: 4444 Forest Park Ave. (5th Floor)

department: Center for Genome Sciences and Systems Biology

institute: Washington University School of Medicine

organism:
Bacteroides thetaiotaomicron VPI-5482
Bacteroides sp. WH2
Blautia obeum ATCC 29174
[Ruminococcus] torques ATCC 27756
Dorea longicatena DSM 13814
[Clostridium] scindens ATCC 35704
Bacteroides ovatus ATCC 8483
Bacteroides uniformis ATCC 8492
Faecalibacterium prausnitzii M21/2
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Thomasclavelia spiroformis DSM 1552
Phocaeicola vulgatus ATCC 8482
Parabacteroides distasonis ATCC 8503
Agathobacter rectalis ATCC 33656

first: Jeffrey

last: Gordon

manufacture_protocol: In situ oligonucleotide synthesis using photolithography.


title: Agilent-019159 Rat miRNA microarray v1.0 (Sanger release 10.1)

status: Public on Mar 15 2012

city: Philadelphia

first: Rachael

last: Dippold

state: PA

address: 1020 Locust St., JAH 222

department: Pathology, Anatomy, and Cell Biology

institute: Thomas Jefferson University

organism: Rattus norvegicus

description: Rat miRNA Microarray 1.0

first: Raj

last: Vadigepalli

first: Greg

last: Gonye

first: Jan

middle: B

last: Hoek


title: NimbleGen Homo sapiens HG18 090828 opt expr HX12 (12x135k)

status: Public on Mar 17 2010

description: NimbleGen design name 090828_HG18_opt_expr_HX12. This is a whole homo sapiens genome array in 12-plex format provided by nimblegen. See manufacturer's website at http://www.nimblegen.com/.


title: Agilent-019597 FHM_Denslow_8x15K [Feature Number version]

status: Public on May 01 2010

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

organism: Pimephales promelas

description: Fathead minnows array with annotated targets. Arrays of this design have barcodes that begin with 16019597 or 2519597.

first: Nancy

middle: D

last: Denslow

first: Li

last: Liu